1 Item carrying capacity
Chris can only carry 6 items, while Jill can carry 8 items. This doesn't include defensive items nor the unique item to each character such as Chris' lighter.
2 Strength and endurance
Chris has a bigger health, he runs faster and is better at aiming at zombies. Jill's health runs out faster and she runs slower.
3 Different special items
Each character has a unique item that they come with. Jill has a lock-pick that allows her to unlock simple locks, whereas Chris has to find an old key for each door. Chris has a lighter as his special item.
4 Differences in story
There are slight differences in the stories of both Characters. Jill is supported by Barry in some situations where Chris gets Rebecca's support. This results in different cut-scenes or each character. Generally Chris gets less assistance than Jill.
5 Different defensive weapons
Chris has an additional weapon, the flash grenade, which is used for last resort defense. Chris might find flash grenades to use them as they are not infinite. Jill on the other hand has a stun-gun which can deal lots of damage to enemies.
6 Different weapons
While Jill gets access to the grenade launcher, she can't get the flamethrower. Chris, on the other hand, can get the flamethrower but can't get access to the grenade launcher.
7 Jill gets the shotgun easier
Because Barry helps Jill with the shotgun puzzle, she is able to get the shotgun without finding the broken shotgun first. See getting the shotgun.
8 It's easier to play with Jill
The game is generally easier to play with Jill because of Barry's support and the fact that she doesn't have to go back and forth to the item box because of her item carrying capacity. In addition to that, the lock-pick she has makes things much easier.